Transcriptomic Survey of How Acetate Addition Affected the Growth in Nannochloropsis oceanica (Suda & Miyashita) R. E. Lee

Nannochloropsis oceanica (Suda & Miyashita) R. E. Lee holds considerable potential for the production of high-value compounds, including pigments, lipids, and polyunsaturated fatty acids. Sodium acetate, a widely used carbon source in microbial cultivation, is both cost-effective and efficient. Although it has been reported to enhance biomass production in various microalgae, its effects on metabolic pathways differ substantially across species. In this study, we investigated the transcriptional responses of N. oceanica to sodium acetate supplementation using high-throughput mRNA sequencing. Sodium acetate significantly promoted growth but elicited a distinct metabolic reprogramming in contrast to patterns commonly observed in other microalgae. We identified 747 differentially expressed genes (399 upregulated and 348 downregulated), reflecting a substantial transcriptomic shift. Pathways related to lipid metabolism, carbon fixation, and photosynthesis were markedly suppressed. Notably, genes associated with photosynthesis were downregulated by 34–43 fold, suggesting a strategic reallocation of resources away from energy-intensive photosynthetic processes in the presence of an external organic carbon source. In sharp contrast to Chlamydomonas reinhardtii P. A. Dangear and Haematococcus pluvialis (Flotow) Wille, lipid metabolism in N. oceanica was not enhanced under sodium acetate supplementation. Instead, expression of lipid metabolism genes decreased by 5–14 fold, with most fatty acid- and lipase-related genes also downregulated (4–30 fold). Together, these findings reveal that N. oceanica adopts a unique adaptive strategy, channeling acetate-derived carbon primarily into rapid biomass accumulation rather than energy storage or high-value metabolite synthesis. This work provides new insights into the species-specific responses of microalgae to organic carbon sources.